The basic steps to use the "visualize data in structure module" are:
- Select one or more structure files from the "select structure" tab
- Select or deselect data (correlated mutations, conservation, contacts and bridges) to visualize the preferred data in the selected structures using the corresponding tabs.
- Click on "Visualize Molecule" to generate a yasara scene. A new page will open which (after a couple of seconds) should show the "Yasara Scene" button.
- Download the yasara scene by clicking the "Yasara Scene" button and open the file with yasara
In the first tab (select structures) different available structures can be selected. ALL STRUCTURES CAN BE COMBINED because all structures are superimposed INCLUDING the co-crystalized compound (e.g inhibitors, substrate analogs, etc).
- Templates: contains the structures that are the templates of the alignment.
- PDB files in alignment: contains structure files that are aligned in one of the subfamilies.
- Non-aligned pdb files: contains structure files that could be superimposed, but were not included in the alignment.*
- Models: contains structure files for any models that have been generated.**
- Organic ligands: contains co-crystalized small organic molecules such as inhibitors, activators, substrate analogs, etc.
- Metal/Ion/Solvent Molecules" Contains solvent molecules such as SO4, glycerol or single atoms (Ions metals).
In the other tabs "correlated mutations", "conservation" and "contacts" different data types can be selected that, after enabling the checkboxes, will be visualized in the structure(s) that are selected in the "select structures" tabs. Note that the correlated mutation data and the conserved residues are selected by default.\
* Why 3DM did not include PDB files in the alignment can have multiple reasons, but mostly this is because the structural similarity is low compared to the other family members.
** To generate models, go to the protein page of the sequence for which a model needs to be generated and click "generate model".